4TU3

Crystal structure of yeast Sac1/Vps74 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Sac1-Vps74 structure reveals a mechanism to terminate phosphoinositide signaling in the Golgi apparatus.

Cai, Y., Deng, Y., Horenkamp, F., Reinisch, K.M., Burd, C.G.

(2014) J Cell Biol 206: 485-491

  • DOI: https://doi.org/10.1083/jcb.201404041
  • Primary Citation of Related Structures:  
    4TU3

  • PubMed Abstract: 

    Sac1 is a phosphoinositide phosphatase of the endoplasmic reticulum and Golgi apparatus that controls organelle membrane composition principally via regulation of phosphatidylinositol 4-phosphate signaling. We present a characterization of the structure of the N-terminal portion of yeast Sac1, containing the conserved Sac1 homology domain, in complex with Vps74, a phosphatidylinositol 4-kinase effector and the orthologue of human GOLPH3. The interface involves the N-terminal subdomain of the Sac1 homology domain, within which mutations in the related Sac3/Fig4 phosphatase have been linked to Charcot-Marie-Tooth disorder CMT4J and amyotrophic lateral sclerosis. Disruption of the Sac1-Vps74 interface results in a broader distribution of phosphatidylinositol 4-phosphate within the Golgi apparatus and failure to maintain residence of a medial Golgi mannosyltransferase. The analysis prompts a revision of the membrane-docking mechanism for GOLPH3 family proteins and reveals how an effector of phosphoinositide signaling serves a dual function in signal termination.

    • Organizational Affiliation: 

    Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoinositide phosphatase SAC1A [auth X]623Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SAC1, RSD1, YKL212W
EC: 3.1.3
UniProt
Find proteins for P32368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32368 
Go to UniProtKB:  P32368
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32368
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 74B [auth A]345Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPS74, YDR372C, D9481.15
UniProt
Find proteins for Q06385 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06385 
Go to UniProtKB:  Q06385
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06385
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.338α = 90
b = 159.338β = 90
c = 143.389γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary